Cell fate reprogramming of erythroid cells caused by reduction of H3K4me3 lead to a “retrograde manner” leukemia genesis [CUT&Tag]

While it's established that methionine metabolism, can impact histone methylation to have a direct role in influencing cell fate determination, methionine metabolic regulation of hematopoietic stem cell commitment and erythroid differentiation is unknown. Here, we investigated how AHCY, an important enzyme in themethionine cycle and timely hydrolysis to sustain methylation reactions, regulates cell fate reprogrammingon in vitro and in vivo. Firstly, we observed that depletion or targeted pharmacological inhibition of AHCY in erythrocytes markedly inhibites cell proliferation, induces cell apoptosis and causes the appearance of other lineage cells. In addition, we applied single-cell sequencing to adherent and suspended cells and identified multiple cell populations, including stem/progenitor cells such as HSC, megakaryocyte/erythroid progenitor cells (MEP), common myeloid progenitor cells (CMP), and granulocyte monocyte progenitor cells (GMP), as well as immune cells such as macrophages and myeloid dendritic cells (mDC). We engrafted adherent and suspended cells into NCG-c-kit-Cas9-TM mice without irradiation. After 4 weeks and 12 weeks postengraftment, we observed human cell chimerism in marrow, peripheral blood and spleen. Importantly, we further found that AHCY-mediated histone methylation rather than DNA methylation leading to cell dedifferentiation including H3K4me3, H3K9me3, H3K27me3, H3K36me2 and H3K79me2 modifications. However, consistent phenotype can be observed only after specific inhibiting H3K4me3 on the terminal erythropoiesis. Integrating CUT&Tag sequencing and RNA-seq analysis revealed that expression of transcription factors(TFs), including those lineage-specific TFs (GATA2, CEBPA), are upregulated in dedifferentiation cells, and erythrocyte lineage-specific TFs (GATA1, KLF1) are significantly downregulated. Because AHCY gene expression was significantly lower in terminal erythroid cells of AML patients compared to healthy individuals, clinically, we next detected relatively low levels of H3K4me3 in erythroblasts from bone marrow of some leukemia patients. Colony formation detection was performed on these erythroblasts in vitro using modified semisolid clonal culture, and multiple CFU colony formation could be observed through morphological verification of colony types. These results reveal a previously unappreciated mechanism of methionine metabolism regulating erythropoiesis by affecting methylation modification. All these findings also reveal that histone methylation landscape reshapes the cell fate decision during human erythropoiesis. And we have demonstrated for the first time that the reduction of H3K4me3 leads to the occurrence of "retrograde" leukemia.